Variant report

Variant	rs7955261
Chromosome Location	chr12:1789371-1789372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1786995..1789598-chr12:1798189..1801520,4	MCF-7	breast:
2	chr12:1783814..1786407-chr12:1787390..1790840,3	MCF-7	breast:
3	chr12:1789009..1790648-chr12:1794138..1796039,2	K562	blood:
4	chr12:1769818..1772528-chr12:1789216..1791447,2	MCF-7	breast:
5	chr12:1782061..1785967-chr12:1788388..1791261,4	K562	blood:
6	chr12:1770836..1772849-chr12:1788601..1790387,2	K562	blood:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1044471	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10735003	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10744551	0.80[EUR][1000 genomes]
rs10773980	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10773988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773989	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs10773991	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848548	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10848550	0.92[CEU][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10848557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10848561	0.84[ASN][1000 genomes]
rs10848563	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10848565	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10848567	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10848571	0.87[ASN][1000 genomes]
rs11061971	0.87[ASN][1000 genomes]
rs11612383	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs11614639	0.84[CEU][hapmap]
rs12316367	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2068485	0.88[CEU][hapmap]
rs2068491	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2108642	0.84[ASN][1000 genomes]
rs2190556	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286383	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2286384	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3759374	0.87[ASN][1000 genomes]
rs4140992	0.91[ASN][1000 genomes]
rs4765843	0.87[ASN][1000 genomes]
rs4765844	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4766415	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6489326	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7138924	0.92[CEU][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7294668	0.88[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs7296521	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315046	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7316218	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7962394	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7974422	0.87[ASN][1000 genomes]
rs7974924	0.87[ASN][1000 genomes]
rs7976827	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978362	0.84[ASN][1000 genomes]
rs7978783	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9300298	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs9739162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9805049	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7955261	CACNA2D4	cis	multi-tissue	Pritchard

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1788000-1789800	Weak transcription	HepG2	liver

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